Comparison of non-coding transcripts from E. coli and Salmonella grown under similar conditions. Transcriptome or Gene expression

The paucity of functionally characterized antisense RNAs (asRNAs) from well-studied species such as E. coli and Salmonella, combined with limited overlap observed between the sets of asRNAs detected by different groups call into question the biological relevance of these putative regulatory elements. Because of the difficulties associated with assaying the phenotypes of thousands of asRNA genome-wide, we applied a comparative approach in which we sequenced in parallel the transcriptomes of E. coli and Salmonella Typhimurium, and identified the most highly expressed transcripts arising from the opposite strand of protein coding genes. Although antisense transcription, like the transcription of protein-coding genes, is often associated with upstream %u03C370 promoters, the majority of asRNAs are not conserved either within or across species. The lack of evolutionary conservation and discordance of expression between the two closely related enteric bacteria indicate that most asRNAs detected solely by deep-sequencing techniques are transient, non-functional transcripts originating from spurious promoter-like sequences that are situated throughout the genome.